17-19585538-A-G

Variant names:

• chr17-19585538-A-G
• rs2453589

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.419 in 151,912 control chromosomes in the GnomAD database, including 13,827 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (13827 hom., cov: 31)
• Consequence: SLC47A1P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 14 publications found

Genes affected

SLC47A1P1 (HGNC:51849): (SLC47A1 pseudogene 1)

ENSG00000290454 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC47A1P1		n.19585538A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290454	ENST00000420951.1	n.272+5203A>G		intron_variant	Intron 2 of 4	5
SLC47A1P1	ENST00000449666.3	n.348-1086A>G		intron_variant	Intron 1 of 7	6
ENSG00000290454	ENST00000454535.5	n.129+3983A>G		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63574 AN: 151792 Hom.: 13795 Cov.: 31

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.418

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.419 AC: 63656 AN: 151912 Hom.: 13827 Cov.: 31 AF XY: 0.423 AC XY: 31379 AN XY: 74250

African (AFR) AF: 0.447 AC: 18495 AN: 41408

American (AMR) AF: 0.548 AC: 8358 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3472

East Asian (EAS) AF: 0.689 AC: 3544 AN: 5144

South Asian (SAS) AF: 0.479 AC: 2305 AN: 4812

European-Finnish (FIN) AF: 0.340 AC: 3592 AN: 10552

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25091 AN: 67950

Other (OTH) AF: 0.420 AC: 885 AN: 2108

Alfa AF: 0.393 Hom.: 40979

Bravo AF: 0.436

Asia WGS AF: 0.559 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.0
DANN	Benign	0.82
PhyloP100		0.11

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2453589; hg19: chr17-19488851;